Hi, Zhen,

It looks a known issue that is fixed in later versions of the package.

You will need to be using a version >= 1.4.1; you can check by typing
"sessionInfo()" into your R terminal.

You will also have to tell AffyTiling not to limit the analysis to NCBI
coordinates.  You can do this by editing your command as follows:
> NORM <- AnalyzeTilingCelFiles(dir(pattern=".cel|.CEL"), *
readOnlyNCBI=FALSE,*
"At35b_MR_v04-2_TIGRv5.bpmap", outfilename="normalizedata.tsv")

Please write back if you continue to have problems!

Good luck!

Best,
Charles



Message: 4
Date: Mon, 28 Dec 2009 15:11:23 +0800
From: zhen tao <jennytz8@gmail.com>
Subject: [BioC] error in AffyTiling package
To: bioconductor@stat.math.ethz.ch
Message-ID:
      <8b7b0b050912272311s3f10fecm2ccab94cfe594261@mail.gmail.com>
Content-Type: text/plain

Hi:

I'm trying to use AffyTiling package to normalize my tiling array data.
However, it shows the error below (hightlighted in yellow) when I run the
function AnalyzeTilingCelFiles. Does anybody know how to deal with this?
Thanks!!!!

> NORM <- AnalyzeTilingCelFiles(dir(pattern=".cel|.CEL"),
"At35b_MR_v04-2_TIGRv5.bpmap", outfilename="normalizedata.tsv")
[1] "Importing BPMAP file."
[1] "Reading CEL Files & Extracting Intensities."
[1] "Quantile normalizing/ log(2) transform."
[1] "Finalizing data."
Error in dimnames(x) <- dn :
length of 'dimnames' [2] not equal to array extent


Tao Zhen
Plant Functional Genomics Group
DBS
NUS


-- 
Postdoctoral Fellow
Cornell University
102D Weill Hall
Ithaca, NY 14853

Phone (Lab, 467 Biotech Bldg.): 607-255-4743
E-mail: dankoc@gmail.com

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